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(-) Description

Title :  ELECTRON CRYO-MICROSCOPY OF HUMAN PAPILLOMAVIRUS 16 AND H16.V5 FAB FRAGMENTS
 
Authors :  H. Lee, S. A. Brendle, S. M. Bywaters, N. D. Christensen, S. Hafenstein
Date :  23 Jun 14  (Deposition) - 26 Nov 14  (Release) - 18 Mar 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  13.60
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L
Biol. Unit 1:  A,B,C,D,E,F,H,L  (60x)
Keywords :  Hpv16. V5 Fab Variable Domain, Hi And Fg Loops, Hpv16 Capsid, Virus- Fab Complex, Neutralization Antibody, Maturation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lee, S. A. Brendle, S. M. Bywaters, J. Guan, R. E. Ashley, J. D. Yoder, A. M. Makhov, J. F. Conway, N. D. Christensen, S. Hafenstein
A Cryo-Electron Microscopy Study Identifies The Complete H16. V5 Epitope And Reveals Global Conformational Changes Initiated By Binding Of The Neutralizing Antibody Fragment.
J. Virol. V. 89 1428 2015
PubMed-ID: 25392224  |  Reference-DOI: 10.1128/JVI.02898-14

(-) Compounds

Molecule 1 - H16.V5 FAB LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: L, A, C, E
    Fragment: VARIABLE DOMAIN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - H16.V5 FAB HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: H, B, D, F
    Fragment: VARIABLE DOMAIN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHL
Biological Unit 1 (60x): ABCDEFHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3J7E)

(-) Sites  (0, 0)

(no "Site" information available for 3J7E)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:94
2B:137 -B:211
3C:23 -C:94
4D:137 -D:211
5E:23 -E:94
6F:137 -F:211
7H:137 -H:211
8L:23 -L:94

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:100 -Pro L:101
3Ser A:7 -Pro A:8
4Thr A:100 -Pro A:101
5Ser C:7 -Pro C:8
6Thr C:100 -Pro C:101
7Ser E:7 -Pro E:8
8Thr E:100 -Pro E:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J7E)

(-) Exons   (0, 0)

(no "Exon" information available for 3J7E)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e A   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLDSRNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPLTFGAGTKLELKRA 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with K7TH34_MOUSE | K7TH34 from UniProtKB/TrEMBL  Length:111

    Alignment length:121
                                    1                                                                                        91  92                  
                                    |2        12        22        32        42        52        62        72        82        |-  |     99       109 
         K7TH34_MOUSE     - --------AELARPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGAIYPGDGDTRYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARD---YGSSYGFAYWGQGTLVTVS 110
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..hhhhh.....ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e B 116 EVKLEQSGAELARPGASVKLSCKASGYTFASYWMQWVKQRPGQGLEWIGAIYPGDGDTWYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARPPYYYGTTYYFDYWGQGTTLTVS 236
                                   125       135       145       155       165       175       185       195       205       215       225       235 


Chain C from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e C   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLDSRNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPLTFGAGTKLELKRA 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with K7TH34_MOUSE | K7TH34 from UniProtKB/TrEMBL  Length:111

    Alignment length:121
                                    1                                                                                        91  92                  
                                    |2        12        22        32        42        52        62        72        82        |-  |     99       109 
         K7TH34_MOUSE     - --------AELARPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGAIYPGDGDTRYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARD---YGSSYGFAYWGQGTLVTVS 110
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..hhhhh.....ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e D 116 EVKLEQSGAELARPGASVKLSCKASGYTFASYWMQWVKQRPGQGLEWIGAIYPGDGDTWYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARPPYYYGTTYYFDYWGQGTTLTVS 236
                                   125       135       145       155       165       175       185       195       205       215       225       235 


Chain E from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e E   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLDSRNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPLTFGAGTKLELKRA 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain F from PDB  Type:PROTEIN  Length:121
 aligned with K7TH34_MOUSE | K7TH34 from UniProtKB/TrEMBL  Length:111

    Alignment length:121
                                    1                                                                                        91  92                  
                                    |2        12        22        32        42        52        62        72        82        |-  |     99       109 
         K7TH34_MOUSE     - --------AELARPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGAIYPGDGDTRYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARD---YGSSYGFAYWGQGTLVTVS 110
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..hhhhh.....ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e F 116 EVKLEQSGAELARPGASVKLSCKASGYTFASYWMQWVKQRPGQGLEWIGAIYPGDGDTWYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARPPYYYGTTYYFDYWGQGTTLTVS 236
                                   125       135       145       155       165       175       185       195       205       215       225       235 


Chain H from PDB  Type:PROTEIN  Length:121
 aligned with K7TH34_MOUSE | K7TH34 from UniProtKB/TrEMBL  Length:111

    Alignment length:121
                                    1                                                                                        91  92                  
                                    |2        12        22        32        42        52        62        72        82        |-  |     99       109 
         K7TH34_MOUSE     - --------AELARPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGAIYPGDGDTRYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARD---YGSSYGFAYWGQGTLVTVS 110
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..hhhhh.....ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e H 116 EVKLEQSGAELARPGASVKLSCKASGYTFASYWMQWVKQRPGQGLEWIGAIYPGDGDTWYTQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARPPYYYGTTYYFDYWGQGTTLTVS 236
                                   125       135       145       155       165       175       185       195       205       215       225       235 


Chain L from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3j7e L   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLDSRNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPLTFGAGTKLELKRA 115
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3J7E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J7E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J7E)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3J7E)

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(no "Sites" information available for 3j7e)
 
  Cis Peptide Bonds
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr A:100 - Pro A:101   [ RasMol ]  
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    Thr E:100 - Pro E:101   [ RasMol ]  
    Thr L:100 - Pro L:101   [ RasMol ]  
 
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 Related Entries

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(-) Related Entries Specified in the PDB File

3j7g